Zinc fingers are among the most common DNA binding motifs found in eukaryotes. It is estimated that there are 500 zinc finger proteins encoded by the yeast genome and that perhaps 1% of all mammalian genes encode zinc finger containing proteins. These proteins are classified according to the number and position of the cysteine and histidine residues available for zinc coordination.
The CCHH class, typified by the Xenopus transcription factor IIIA (19), is the largest. These proteins contain two or more fingers in tandem repeats. In contrast, the steroid receptors contain only cysteine residues that form two types of zinc-coordinated structures with four (C4) and five (C5) cysteines (28). Another class of zinc fingers contains the CCHC fingers. The CCHC fingers, which are found in Drosophila, and in mammalian and retroviral proteins, display the consensus sequence C-N2-C-N4-H-N4-C (SEQ ID NO:65) (Refs. 7, 21, 24). Recently, a novel configuration of CCHC finger, of the C-N5-C-N12-H-N4-C (SEQ ID NO:66) type, was found in the neural zinc finger factor/myelin transcription factor family (Refs. 11, 12, 36). Finally, several yeast transcription factors such as GAL4 and CHA4 contain an atypical C6 zinc finger structure that coordinates two zinc ions (Refs. 9, 32).
Zinc fingers are usually found in multiple copies (up to 37) per protein. These copies can be organized in a tandem array, forming a single cluster or multiple clusters, or they can be dispersed throughout the protein. Several families of transcription factors share the same overall structure by having two (or three) widely separated clusters of zinc fingers in their protein sequence. The first, the MBPs/PRDII-BF1 transcription factor family, includes Drosophila Schnurri and Spalt genes (1, 3, 6, 14, 33). Both MBP-1 (also known as PRDII-BF1) and MBP-2 contain two widely separated clusters of two CCHH zinc fingers. The overall similarity between MBP-1 and MBP-2 is 51%, but the conservation is much higher (over 90%) for both the N-terminal and the C-terminal zinc finger clusters (33). This indicates an important role of both clusters in the function of these proteins. In addition, the N-terminal and C-terminal zinc finger clusters of MBP-1 are very homologous to each other (3).
The neural specific zinc finger factor 1 and factor 3 (NZF-1 and NZF-3), as well as the myelin transcription factor 1 (MyT1, also known as NZF-2), belong to another family of proteins containing two widely separated clusters of CCHC zinc fingers (11, 12, 36). Like the MBP proteins, different NZF factors exhibit a high degree of sequence identity (over 80%) between the respective zinc finger clusters, whereas the sequences outside of the zinc finger region are largely divergent (36). In addition, each of these clusters can independently bind to DNA, and recognizes similar core consensus sequences (11). NZF-3 binds to a DNA element containing a single copy of this consensus sequence but was shown to exhibit a marked enhancement in relative affinity to a bipartite element containing two copies of this sequence (36). This finding suggests that the NZF factors may also bind to reiterated sequences. However, the mechanism underlying the cooperative binding of NZF-3 to the bipartite element is currently unknown.
The Drosophila Zjh-1 and the vertebrate δEF1 proteins (also known as ZEB or AREB6) belong to a third family of transcription factors. This family is characterized by the presence of two separated clusters of CCHH zinc fingers and a homeodomain-like structure (see, FIG. 1A) (Refs. 4, 5, 35). In δEF1, the N-terminal and C-terminal clusters are also very homologous and were shown to bind independently to very similar core consensus sequences (10). Recently, it was shown that mutant forms of δEF1 lacking either the N-terminal or the C-terminal cluster have lost their DNA binding capacity indicating that both clusters are required for the binding of δEF1 to DNA (31). The Evi-1 transcription factor was shown to contain ten CCHH zinc fingers; seven zinc fingers are present in the N-terminal region, and three zinc fingers are in the C-terminal region (22). With this factor the situation is different from the transcription factors described above, because the two clusters bind to two different target sequences, which are bound simultaneously by full-length Evi-1 (20). Binding of full-length Evi-1 is mainly observed when the two target sequences are positioned in a certain relative orientation, but there was no strict requirement for an optimal spacing between these two targets.
Cell-cell adhesion is predominantly a necessity during cell differentiation, tissue development, and tissue homeostasis. The effect of disrupted cell-cell adhesion is displayed in many cancers, where metastasis and poor prognosis are correlated with loss of cell-cell adhesion. E-cadherin, a homophilic Ca2+-dependent transmembrane adhesion molecule, and the associated catenins are among the major constituents of the epithelial cell-junction system. E-cadherin exerts a potent invasion-suppressing role in tumor cell line systems (Refs. 46, 47) and in in vivo tumor model systems (Ref. 48). Loss of E-cadherin expression during tumor progression has been described for more than 15 different carcinoma types (49). Extensive analyses has made clear that aberrant E-cadherin expression as a result of somatic inactivating mutations of both E-cadherin alleles is rare and so far largely confined to diffuse gastric carcinomas and infiltrative lobular breast carcinomas (50, 51). Northern analysis and in situ hybridization studies revealed that reduced E-cadherin immunoreactivity in human carcinomas correlates with decreased mRNA levels (52-54). Analysis of mouse and human E-cadherin promoter sequences revealed a conserved modular structure with positive regulatory elements including a CCAAT-box and a GC-box, as well as two E-boxes (CANNTG) with a potential repressor role (Refs. 55, 56). Mutation analysis of the two E-boxes in the E-cadherin promoter demonstrated a crucial role in the regulation of the epithelial specific expression of E-cadherin. Mutation of these two E-box elements results in the up regulation of the E-cadherin promoter in dedifferentiated cancer cells, where the wild-type promoter shows low activity (55, 56).